Gene multifunctionality scoring using gene ontology

NONMMUT140591.1 may serve as a ceRNA to regulate Gata5 in UT-B knockout-induced cardiac conduction block

We intended to explore the potential molecular mechanisms underlying the cardiac conduction block inducted by urea transporter (UT)-B deletion at the transcriptome level. The heart tissues were harvested from UT-B null mice and age-matched wild-type mice for lncRNA sequencing analysis. Based on the sequencing data, the differentially expressed mRNAs (DEMs) and lncRNAs (DELs) between UT-B knockout and control groups were identified, followed by function analysis and mRNA-lncRNA co-expression analysis. The miRNAs were predicted, and then the competing endogenous RNA (ceRNA) network was constructed. UT-B deletion results in the aberrant expression of 588 lncRNAs and 194 mRNAs. These DEMs were significantly enriched in the inflammation-related pathway. A lncRNA-mRNA co-expression network and a ceRNA network were constructed on the basis of the DEMs and DELs. The complement 7 (C7)-NONMMUT137216.1 co-expression pair had the highest correlation coefficient in the co-expression network. NONMMUT140591.1 had the highest degree in the ceRNA network and was involved in the ceRNA of NONMMUT140591.1-mmu-miR-298-5p-Gata5 (GATA binding protein 5). UT-B deletion may promote cardiac conduction block via inflammatory process. The ceRNA NONMMUT140591.1-mmu-miR-298-5p-Gata5 may be a potential molecular mechanism of UT-B knockout-induced cardiac conduction block.

Bioinformatic evidences and analysis of putative biomarkers in pancreatic ductal adenocarcinoma

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal human cancers. Aberrant expression of genes plays important role in the procession of PDAC. The analysis of gene expression profile will contribute to the research of carcinoma mechanism.

OBJECTIVE

This present study is focused to investigate the differentially expressed genes (DEGs) from 3 PDAC microarray datasets, which would provide candidate genes for putative biomarkers to understand the mechanism of PDAC and potential targets of treatment.

METHOD

Based on the overlap genes obtained from 3 GEO datasets, the hub genes were identified using STRING and Cytoscape plugin MCODE. The enrichment and function analysis were applied using DAVID. The protein-protein interaction network was performed using cBioPortal and UCSC Xena. The Oncomine was finally used to determine the candidate gene by analyzing their expression between pancreas sample and PDAC sample.

RESULTS

25 hub genes were selected from a total of 1006 DEGs from 3 GEO datasets, consisting of 14 upregulated genes and 11 downregulated genes. The overall decline of hub gene expression enriched in G1 phase of cell cycle in other subtypes of pancreatic cancer. Oncomine database was ultimately performed to determine the 8 candidate genes, including CXCL5, CCL20, NMU, F2R, ANXA1, EDNRA, LPAR6, and GNA15.

CONCLUSIONS

Conclusively, 8 candidate genes would become the potential PDAC combined biomarkers for diagnosis and therapeutic strategies.

Screening of key miRNAs and evaluation of their diagnostic and prognostic values in nasopharyngeal carcinoma

Increasing evidence has revealed the importance of microRNA (miRNA/miR) in cancer genesis and progression. The aim of the current study was to identify the key miRNAs involved in the onset and development of nasopharyngeal carcinoma (NPC) and to further evaluate their diagnostic and prognostic values. Microarray data were obtained and analyzed to screen differentially expressed miRNAs (DEMs) between patients with NPC and healthy controls. The target genes of the DEMs were predicted and their possible functions were evaluated. The diagnostic and prognostic values of the DEMs were subsequently investigated. A total of 4 DEMs, including miR-18a, miR-135b, miR-204 and miR-497, were identified. Gene Ontology (GO) and pathway enrichment analysis revealed that the target genes were enriched in a number of GO terms and signaling pathways. The results demonstrated that the selected DEMs may present potential diagnostic factors for NPC. In addition, miR-18a [Hazard ratio (HR), 3.405; 95% confidence interval (CI), 1.334-8.693] and miR-135b (HR, 2.482; 95% CI, 1.014-6.076) may serve prognostic roles for patients with NPC. In summary, the present study identified 4 miRNAs that may be involved in the genesis and development of NPC. In addition, miR-18a and miR-135b may present useful prognostic markers for patients with NPC. Future in vitro and in vivo investigations are warranted to substantiate the results obtained in the current study.